EdgeR - default offset

[drea11]

Greetings R aficionados!

I was wondering whether anyone could tell me what the default offset is that is used in the glmFit function of EdgeR? Is it either the library size, or lib.size*norm.factor(from calcNormFactors)?

Thanks for the help!

[dpryan]

From the source code:

#       Check offset and lib.size
        if(is.null(offset)) {
                if(is.null(lib.size)) lib.size <- colSums(y)
                offset <- log(lib.size)
        }

So, log(lib.size).

[Gordon Smyth]

If y is a matrix, then offset defaults to log(lib.size).

If y is a DGEList, then offset defaults to y$offset if that is set, otherwise to log(lib.size*norm.factors). See getOffset.

In other words, it defaults to whatever can be found in y.

[drea11]

Thank you!